qiime diversity alpha-group-significance

[Muhammad_Arslan]

I am trying to run the following command for diversity analysis:
qiime diversity alpha-group-significance \
--i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
--m-metadata-file metadata.tsv \
--o-visualization core-metrics-results/faith_pd_group_significance

But I am getting this error
(1/4) Missing option "--i-alpha-diversity".
(2/4) Missing option "--m-metadata-file".
(3/4) Missing option "--o-visualization". ("--output-dir" may also be used)
(4/4) Got unexpected extra arguments ( --i-alpha-diversity core-metrics-
results/faith_pd_vector.qza --m-metadata-file metadata.tsv
--o-visualization core-metrics-results/faith)

Can someone comment? Thank you very much in advance!

[Muhammad_Arslan]

I just realized that none of the QIIME diversity analysis are running. I am not sure what is the error! I need help!

[Mehrbod_Estaki]

Hi @Muhammad_Arslan,
Looks to me this is an issue with text formatting in your commands. Are you copy & pasting these from another text editor by chance, like word or something else? Those tend to mess up text with unwanted special characters, say by converting 2 small dashes to a long dash.
So what you want to type is:

qiime diversity alpha-group-significance \
  --i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization core-metrics-results/faith-pd-group-significance.qzv

Note the difference between the two -- and the – your command has.
Give that a try!

[Muhammad_Arslan]

Oh. This worked perfectly. Thanks for commenting. You are right as I used BBedit to write codes which I then paste in the terminal.
Thanks again!
Best